Retrieving reference data tracks

For most applications (except de novo sequencing), you will need reference data in the form of a reference genome sequence, annotations, known variants etc. There are three basic ways of obtaining tracks with reference data:
  1. Use the integrated tool for downloading reference genomes as tracks.
  2. Import tracks from files (learn more in Import tracks from file).
  3. Convert sequences with annotations to tracks (learn more in Converting data to tracks and back). Sequences can come from a variety of sources:
    Standard Import (Image import)
    The standard import accepts common data formats like fasta, genbank etc. (learn more in Bioinformatic data formats)
    Downloading from NCBI
    The integrated tool for searching and downloading data from NCBI (learn more in GenBank search).
    Contigs created from de novo assembly
    . Contig sequences from (de novo assembly can be considered a reference genome for e.g. subsequent resequencing analysis applications.
  4. Use the special plug-ins that integrate with Biobase's Genome Trax (learn more at
Please note that tracks are not yet supported with the transcriptomics tools of CLC Genomics Workbench. This means you have to provide standard sequences (downloading from NCBI or importing files).